Background: There is a growing interest in utilizing endophytes as biofertilizers or biological controls. Beneficial effects may be obtained by synthesizing phytohormones, enzymes and antagonistic substances, fixing nitrogen and carbon dioxide, inducing defence mechanisms and competing colonizing sites and nutrients. Endophytes enhance plant growth and health through plant growth promoting rhizobacteria. Endophytes enter plant tissues through root zone or aerial portions, via germinating radicles, secondary roots, stomata, or foliar route. Endophyte-plant-polymer degrading enzymes such as cellulases and pectinases play a role for their internal colonization and can be detected by immunological or in situ hybridization or tagging with reporter genes. Endophytes interact biochemically and genetically with their host plant and synthesize osmolytes, osmoprotectants, antioxidants, allowing the plants to mitigate the impacts of abiotic stress. Plant genes are modulated by endophyte, and the genes so expressed provide clues as to the effects of endophytes in plants.Objective: The present review describes bioprospecting of endophyte-plant interactions and discusses the way forward to understand their molecular mechanisms. Conclusion: Endophytes are useful models to study the genetic expression of microbe inside the plants, which are well-regulated and flexible. This helps in developing effective endophyte bioinoculants for abiotic stress and crop disease management.